chr10-6136273-G-A

Variant names:

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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928080	XR_930619.3	n.614+4745C>T		intron_variant	Intron 1 of 2
LOC101928080	XR_930620.3	n.614+4745C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309490	ENST00000841432.1	n.621+4745C>T		intron_variant	Intron 1 of 1
ENSG00000309490	ENST00000841433.1	n.618+4745C>T		intron_variant	Intron 1 of 2
ENSG00000309490	ENST00000841434.1	n.752+4592C>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs7099083; hg19: chr10-6178236; COSMIC: COSV68210708;