XR_002956539.2:n.442-41369T>C

Variant names:

• chr7-7335192-T-C
• rs6955140
• XR_002956539.2:n.442-41369T>C

Variant summary

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

The XR_002956539.2(LOC107986764):​n.442-41369T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 152,022 control chromosomes in the GnomAD database, including 46,884 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 0.78 (46884 hom., cov: 31)
• Consequence: LOC107986764 XR_002956539.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 1 publications found

Genes affected

LOC107986764 (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 (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986764	XR_002956539.2	n.442-41369T>C		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119141 AN: 151904 Hom.: 46843 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.784 AC: 119236 AN: 152022 Hom.: 46884 Cov.: 31 AF XY: 0.790 AC XY: 58670 AN XY: 74276

African (AFR) AF: 0.748 AC: 31023 AN: 41454

American (AMR) AF: 0.811 AC: 12387 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2685 AN: 3468

East Asian (EAS) AF: 0.879 AC: 4534 AN: 5158

South Asian (SAS) AF: 0.829 AC: 3989 AN: 4814

European-Finnish (FIN) AF: 0.819 AC: 8660 AN: 10576

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53338 AN: 67960

Other (OTH) AF: 0.779 AC: 1644 AN: 2110

Alfa AF: 0.785 Hom.: 10755

Bravo AF: 0.781

Asia WGS AF: 0.859 AC: 2988 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	4.2
DANN	Benign	0.46
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs6955140; hg19: chr7-7374823;