chr10-59448533-G-C

Variant names:

• chr10-59448533-G-C
• rs7911563
• ENST00000796729.1:n.461+31005C>G

Variant summary

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

The ENST00000796729.1(ENSG00000303721):​n.461+31005C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,960 control chromosomes in the GnomAD database, including 20,371 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 0.51 (20371 hom., cov: 32)
• Consequence: ENSG00000303721 ENST00000796729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 1 publications found

Genes affected

ENSG00000303721 (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 (NFE) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796729.1. 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
	ENSG00000303721	ENST00000796729.1		n.461+31005C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77424 AN: 151842 Hom.: 20381 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.509 AC: 77422 AN: 151960 Hom.: 20371 Cov.: 32 AF XY: 0.505 AC XY: 37520 AN XY: 74268

African (AFR) AF: 0.398 AC: 16507 AN: 41462

American (AMR) AF: 0.456 AC: 6954 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2127 AN: 3466

East Asian (EAS) AF: 0.574 AC: 2967 AN: 5170

South Asian (SAS) AF: 0.510 AC: 2452 AN: 4808

European-Finnish (FIN) AF: 0.482 AC: 5075 AN: 10524

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39433 AN: 67950

Other (OTH) AF: 0.552 AC: 1167 AN: 2114

Alfa AF: 0.525 Hom.: 2583

Bravo AF: 0.503

Asia WGS AF: 0.490 AC: 1704 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.47
PhyloP100		-0.13

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: rs7911563;

hg19: chr10-61208291;