rs10049211

Variant names:

• chr3-72465525-T-C
• rs10049211
• ENST00000810549.1:n.412+6400T>C

Variant summary

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

The ENST00000810549.1(ENSG00000305353):​n.412+6400T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,938 control chromosomes in the GnomAD database, including 13,171 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 0.41 (13171 hom., cov: 31)
• Consequence: ENSG00000305353 ENST00000810549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 4 publications found

Genes affected

ENSG00000305353 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810549.1. 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
	ENSG00000305353	ENST00000810549.1		n.412+6400T>C		intron	N/A
	ENSG00000305353	ENST00000810550.1		n.371+6400T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62109 AN: 151818 Hom.: 13142 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.409 AC: 62181 AN: 151938 Hom.: 13171 Cov.: 31 AF XY: 0.400 AC XY: 29684 AN XY: 74262

African (AFR) AF: 0.499 AC: 20667 AN: 41426

American (AMR) AF: 0.361 AC: 5514 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3472

East Asian (EAS) AF: 0.252 AC: 1299 AN: 5154

South Asian (SAS) AF: 0.327 AC: 1573 AN: 4816

European-Finnish (FIN) AF: 0.303 AC: 3196 AN: 10556

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26807 AN: 67928

Other (OTH) AF: 0.437 AC: 921 AN: 2106

Alfa AF: 0.406 Hom.: 3614

Bravo AF: 0.418

Asia WGS AF: 0.337 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.9
DANN	Benign	0.56
PhyloP100		-0.32

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: rs10049211;

hg19: chr3-72514676;