6-43799966-C-T

Variant names:

• chr6-43799966-C-T
• rs10948095
• ENST00000719551.1:n.192+2616C>T

Variant summary

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

The ENST00000719551.1(ENSG00000283573):​n.192+2616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,778 control chromosomes in the GnomAD database, including 22,257 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 (22257 hom., cov: 31)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 8 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719551.1. 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
	ENSG00000283573	ENST00000719551.1		n.192+2616C>T		intron	N/A
	ENSG00000283573	ENST00000719553.1		n.192+2616C>T		intron	N/A
	ENSG00000283573	ENST00000719555.1		n.159+2616C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77988 AN: 151660 Hom.: 22254 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.514 AC: 78001 AN: 151778 Hom.: 22257 Cov.: 31 AF XY: 0.520 AC XY: 38571 AN XY: 74174

African (AFR) AF: 0.241 AC: 9955 AN: 41294

American (AMR) AF: 0.573 AC: 8743 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2304 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3208 AN: 5148

South Asian (SAS) AF: 0.691 AC: 3320 AN: 4802

European-Finnish (FIN) AF: 0.641 AC: 6760 AN: 10552

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41662 AN: 67938

Other (OTH) AF: 0.539 AC: 1133 AN: 2102

Alfa AF: 0.581 Hom.: 64920

Bravo AF: 0.497

Asia WGS AF: 0.613 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.079

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: rs10948095;

hg19: chr6-43767703;