rs12681420

Variant names:

• chr8-70680963-A-G
• rs12681420
• NM_001011720.2:c.-96A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-70680963-A-G
• chr8-70680963-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001011720.2(XKR9):​c.-96A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,144,236 control chromosomes in the GnomAD database, including 87,573 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.33 (9415 hom., cov: 32)
  • Exomes 𝑓: 0.38 (78158 hom.)
• Consequence: XKR9 NM_001011720.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 21 publications found

Genes affected

XKR9 (HGNC:20937): (XK related 9) Predicted to enable phospholipid scramblase activity. Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285579 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR9	NM_001011720.2	c.-96A>G		5_prime_UTR_variant	Exon 3 of 5	ENST00000408926.8	NP_001011720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR9	ENST00000408926.8	c.-96A>G		5_prime_UTR_variant	Exon 3 of 5	1	NM_001011720.2	ENSP00000386141.3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50166 AN: 151832 Hom.: 9413 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.384 AC: 380617 AN: 992286 Hom.: 78158 Cov.: 13 AF XY: 0.379 AC XY: 188380 AN XY: 497198

African (AFR) AF: 0.185 AC: 4249 AN: 22980

American (AMR) AF: 0.226 AC: 5501 AN: 24294

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 5713 AN: 17480

East Asian (EAS) AF: 0.102 AC: 3682 AN: 36112

South Asian (SAS) AF: 0.179 AC: 10324 AN: 57530

European-Finnish (FIN) AF: 0.451 AC: 18313 AN: 40650

Middle Eastern (MID) AF: 0.353 AC: 1065 AN: 3016

European-Non Finnish (NFE) AF: 0.424 AC: 316478 AN: 746362

Other (OTH) AF: 0.349 AC: 15292 AN: 43862

GnomAD4 genome AF: 0.330 AC: 50175 AN: 151950 Hom.: 9415 Cov.: 32 AF XY: 0.328 AC XY: 24372 AN XY: 74250

African (AFR) AF: 0.197 AC: 8162 AN: 41534

American (AMR) AF: 0.286 AC: 4360 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3464

East Asian (EAS) AF: 0.0613 AC: 318 AN: 5184

South Asian (SAS) AF: 0.163 AC: 786 AN: 4818

European-Finnish (FIN) AF: 0.465 AC: 4896 AN: 10520

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.431 AC: 29269 AN: 67870

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.378 Hom.: 16151

Bravo AF: 0.309

Asia WGS AF: 0.134 AC: 467 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.61
PhyloP100		0.18
Mutation Taster		=299/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12681420; hg19: chr8-71593198;