rs6701608

Variant names:

• chr1-90403670-A-C
• rs6701608
• ENST00000653744.1:n.171-2543T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-90403670-A-C
• chr1-90403670-A-G
• chr1-90403670-A-T

Variant summary

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

The ENST00000653744.1(ENSG00000287372):​n.171-2543T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,794 control chromosomes in the GnomAD database, including 29,108 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 0.61 (29108 hom., cov: 31)
• Consequence: ENSG00000287372 ENST00000653744.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 2 publications found

Genes affected

ENSG00000287372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 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
ENSG00000287372	ENST00000653744.1	n.171-2543T>G		intron_variant	Intron 1 of 2
ENSG00000287372	ENST00000655087.1	n.420-2543T>G		intron_variant	Intron 1 of 1
ENSG00000299349	ENST00000762792.1	n.158+18559A>C		intron_variant	Intron 2 of 2
ENSG00000287372	ENST00000762859.1	n.108+16308T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91896 AN: 151676 Hom.: 29104 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.606 AC: 91923 AN: 151794 Hom.: 29108 Cov.: 31 AF XY: 0.601 AC XY: 44545 AN XY: 74178

African (AFR) AF: 0.462 AC: 19116 AN: 41372

American (AMR) AF: 0.667 AC: 10147 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2183 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1098 AN: 5168

South Asian (SAS) AF: 0.570 AC: 2743 AN: 4814

European-Finnish (FIN) AF: 0.615 AC: 6460 AN: 10512

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47914 AN: 67938

Other (OTH) AF: 0.639 AC: 1341 AN: 2098

Alfa AF: 0.664 Hom.: 15428

Bravo AF: 0.603

Asia WGS AF: 0.423 AC: 1478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.72
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs6701608; hg19: chr1-90869227;