rs10229692

Variant names:

• chr7-148422604-G-A
• rs10229692
• ENST00000715351.1:n.297+4886C>T

Variant summary

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

The ENST00000715351.1(ENSG00000287636):​n.297+4886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,964 control chromosomes in the GnomAD database, including 4,988 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 0.19 (4988 hom., cov: 32)
• Consequence: ENSG00000287636 ENST00000715351.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 1 publications found

Genes affected

ENSG00000287636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715351.1. 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
	ENSG00000287636	ENST00000715351.1		n.297+4886C>T		intron	N/A
	ENSG00000287636	ENST00000715352.1		n.299-27912C>T		intron	N/A
	ENSG00000287636	ENST00000715445.1		n.209+13955C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29128 AN: 151846 Hom.: 4983 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.192 AC: 29162 AN: 151964 Hom.: 4988 Cov.: 32 AF XY: 0.187 AC XY: 13923 AN XY: 74306

African (AFR) AF: 0.464 AC: 19209 AN: 41366

American (AMR) AF: 0.102 AC: 1555 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.100 AC: 483 AN: 4820

European-Finnish (FIN) AF: 0.0848 AC: 896 AN: 10566

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0914 AC: 6214 AN: 67978

Other (OTH) AF: 0.166 AC: 350 AN: 2108

Alfa AF: 0.0999 Hom.: 971

Bravo AF: 0.205

Asia WGS AF: 0.0730 AC: 254 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-1.1

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: rs10229692;

hg19: chr7-148119696;