rs7849941

Variant names:

• chr9-85130318-A-T
• rs7849941
• XR_001746807.1:n.191+12127T>A

Variant summary

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

The XR_001746807.1(LOC107987088):​n.191+12127T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,102 control chromosomes in the GnomAD database, including 7,883 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 0.26 (7883 hom., cov: 32)
• Consequence: LOC107987088 XR_001746807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 1 publications found

Genes affected

LOC107987088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987088	XR_001746807.1	n.191+12127T>A		intron_variant	Intron 1 of 3
LOC107987088	XR_001746808.1	n.191+12127T>A		intron_variant	Intron 1 of 3
LOC107987088	XR_001746809.1	n.191+12127T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39290 AN: 151984 Hom.: 7853 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.225

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.259 AC: 39361 AN: 152102 Hom.: 7883 Cov.: 32 AF XY: 0.255 AC XY: 18957 AN XY: 74370

African (AFR) AF: 0.564 AC: 23359 AN: 41424

American (AMR) AF: 0.162 AC: 2470 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3472

East Asian (EAS) AF: 0.0458 AC: 237 AN: 5178

South Asian (SAS) AF: 0.185 AC: 891 AN: 4810

European-Finnish (FIN) AF: 0.171 AC: 1810 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9513 AN: 68008

Other (OTH) AF: 0.223 AC: 470 AN: 2110

Alfa AF: 0.210 Hom.: 666

Bravo AF: 0.272

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7849941; hg19: chr9-87745233;