rs7453655

Variant names:

• chr6-170177401-G-A
• rs7453655
• ENST00000691159.1:n.357+8406C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-170177401-G-A
• chr6-170177401-G-C
• chr6-170177401-G-T

Variant summary

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

The ENST00000691159.1(ENSG00000230960):​n.357+8406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.089 (536 hom., cov: 20)
• Consequence: ENSG00000230960 ENST00000691159.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983
• Publications: 2 publications found

Genes affected

ENSG00000230960 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230960	ENST00000691159.1	n.357+8406C>T		intron_variant	Intron 2 of 2
ENSG00000230960	ENST00000701993.1	n.382+8337C>T		intron_variant	Intron 2 of 2
ENSG00000230960	ENST00000843770.1	n.475+8406C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 7673 AN: 86598 Hom.: 534 Cov.: 20

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0103

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0449

Gnomad EAS AF: 0.00216

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0886 AC: 7678 AN: 86658 Hom.: 536 Cov.: 20 AF XY: 0.0875 AC XY: 3659 AN XY: 41834

African (AFR) AF: 0.108 AC: 2505 AN: 23090

American (AMR) AF: 0.103 AC: 815 AN: 7914

Ashkenazi Jewish (ASJ) AF: 0.0449 AC: 95 AN: 2118

East Asian (EAS) AF: 0.00217 AC: 7 AN: 3230

South Asian (SAS) AF: 0.104 AC: 269 AN: 2582

European-Finnish (FIN) AF: 0.0469 AC: 266 AN: 5668

Middle Eastern (MID) AF: 0.203 AC: 26 AN: 128

European-Non Finnish (NFE) AF: 0.0889 AC: 3583 AN: 40308

Other (OTH) AF: 0.0944 AC: 107 AN: 1134

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		-0.98

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7453655; hg19: chr6-170492625;