rs10487505

Variant names:

• chr7-128220110-G-C
• rs10487505
• ENST00000710955.1:n.836-3923G>C

Your query was ambiguous. Multiple possible variants found:

• chr7-128220110-G-C
• chr7-128220110-G-T

Variant summary

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

The ENST00000710955.1(ENSG00000292309):​n.836-3923G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,004 control chromosomes in the GnomAD database, including 17,920 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 0.48 (17920 hom., cov: 32)
• Consequence: ENSG00000292309 ENST00000710955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 33 publications found

Genes affected

ENSG00000292309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000710955.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000292309	ENST00000710955.1		n.836-3923G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73014 AN: 151886 Hom.: 17913 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.481 AC: 73054 AN: 152004 Hom.: 17920 Cov.: 32 AF XY: 0.482 AC XY: 35838 AN XY: 74322

African (AFR) AF: 0.437 AC: 18115 AN: 41442

American (AMR) AF: 0.436 AC: 6663 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1605 AN: 3468

East Asian (EAS) AF: 0.707 AC: 3654 AN: 5170

South Asian (SAS) AF: 0.444 AC: 2140 AN: 4816

European-Finnish (FIN) AF: 0.548 AC: 5794 AN: 10580

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33496 AN: 67948

Other (OTH) AF: 0.491 AC: 1032 AN: 2102

Alfa AF: 0.476 Hom.: 2151

Bravo AF: 0.469

Asia WGS AF: 0.581 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.40
PhyloP100		0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10487505;

hg19: chr7-127860163;