rs7099083

Variant names:

• chr10-6136273-G-A
• rs7099083
• ENST00000841432.1:n.621+4745C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-6136273-G-A
• chr10-6136273-G-C

Variant summary

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

The ENST00000841432.1(ENSG00000309490):​n.621+4745C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,840 control chromosomes in the GnomAD database, including 14,175 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 0.43 (14175 hom., cov: 31)
• Consequence: ENSG00000309490 ENST00000841432.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 8 publications found

Genes affected

ENSG00000309490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841432.1. 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
	ENSG00000309490	ENST00000841432.1		n.621+4745C>T		intron	N/A
	ENSG00000309490	ENST00000841433.1		n.618+4745C>T		intron	N/A
	ENSG00000309490	ENST00000841434.1		n.752+4592C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65245 AN: 151722 Hom.: 14163 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.430 AC: 65299 AN: 151840 Hom.: 14175 Cov.: 31 AF XY: 0.428 AC XY: 31727 AN XY: 74180

African (AFR) AF: 0.389 AC: 16103 AN: 41404

American (AMR) AF: 0.475 AC: 7257 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2003 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1790 AN: 5156

South Asian (SAS) AF: 0.400 AC: 1917 AN: 4798

European-Finnish (FIN) AF: 0.408 AC: 4299 AN: 10524

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30301 AN: 67908

Other (OTH) AF: 0.472 AC: 996 AN: 2108

Alfa AF: 0.443 Hom.: 7768

Bravo AF: 0.437

Asia WGS AF: 0.369 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.74
PhyloP100		0.34

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: rs7099083;

hg19: chr10-6178236;

COSMIC: COSV68210708;