rs7001819

Variant names:

• chr8-11792966-T-C
• rs7001819
• XR_948962.4:n.44-4899A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-11792966-T-C
• chr8-11792966-T-G

Variant summary

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

The XR_948962.4(LOC105379243):​n.44-4899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,100 control chromosomes in the GnomAD database, including 9,394 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 0.35 (9394 hom., cov: 33)
• Consequence: LOC105379243 XR_948962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 16 publications found

Genes affected

LOC105379243 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379243	XR_948962.4	n.44-4899A>G		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53225 AN: 151982 Hom.: 9388 Cov.: 33

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.350 AC: 53241 AN: 152100 Hom.: 9394 Cov.: 33 AF XY: 0.343 AC XY: 25487 AN XY: 74350

African (AFR) AF: 0.332 AC: 13761 AN: 41488

American (AMR) AF: 0.308 AC: 4706 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1464 AN: 3470

East Asian (EAS) AF: 0.343 AC: 1776 AN: 5180

South Asian (SAS) AF: 0.246 AC: 1189 AN: 4828

European-Finnish (FIN) AF: 0.308 AC: 3249 AN: 10556

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25876 AN: 67982

Other (OTH) AF: 0.367 AC: 775 AN: 2114

Alfa AF: 0.369 Hom.: 23402

Bravo AF: 0.350

Asia WGS AF: 0.272 AC: 941 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7001819; hg19: chr8-11650475;