chr7-41439010-G-A

Variant names:

• chr7-41439010-G-A
• rs10486715
• ENST00000813847.1:n.277+9870C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000813847.1(ENSG00000305895):​n.277+9870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,168 control chromosomes in the GnomAD database, including 3,619 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 0.14 (3619 hom., cov: 33)
• Consequence: ENSG00000305895 ENST00000813847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 6 publications found

Genes affected

ENSG00000305895 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305895	ENST00000813847.1	n.277+9870C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21055 AN: 152050 Hom.: 3597 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.139 AC: 21106 AN: 152168 Hom.: 3619 Cov.: 33 AF XY: 0.134 AC XY: 9982 AN XY: 74406

African (AFR) AF: 0.401 AC: 16616 AN: 41432

American (AMR) AF: 0.0524 AC: 802 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0136 AC: 47 AN: 3466

East Asian (EAS) AF: 0.184 AC: 953 AN: 5166

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4828

European-Finnish (FIN) AF: 0.0260 AC: 276 AN: 10620

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0297 AC: 2023 AN: 68026

Other (OTH) AF: 0.100 AC: 212 AN: 2114

Alfa AF: 0.0664 Hom.: 3600

Bravo AF: 0.154

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	19
DANN	Benign	0.70
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs10486715; hg19: chr7-41478608; COSMIC: COSV63943843;