rs701665

Variant names:

• chr6-68184818-C-T
• rs701665
• ENST00000718116.1:n.418-37851C>T

Variant summary

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

The ENST00000718116.1(ENSG00000285838):​n.418-37851C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,692 control chromosomes in the GnomAD database, including 8,252 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 0.32 (8252 hom., cov: 32)
• Consequence: ENSG00000285838 ENST00000718116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

Genes affected

ENSG00000285838 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 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
ENSG00000285838	ENST00000718116.1	n.418-37851C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48933 AN: 151574 Hom.: 8257 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0983

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.323 AC: 48945 AN: 151692 Hom.: 8252 Cov.: 32 AF XY: 0.322 AC XY: 23828 AN XY: 74096

African (AFR) AF: 0.266 AC: 11002 AN: 41392

American (AMR) AF: 0.327 AC: 4966 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 714 AN: 3462

East Asian (EAS) AF: 0.0986 AC: 509 AN: 5164

South Asian (SAS) AF: 0.207 AC: 998 AN: 4814

European-Finnish (FIN) AF: 0.457 AC: 4802 AN: 10516

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24985 AN: 67830

Other (OTH) AF: 0.285 AC: 601 AN: 2106

Alfa AF: 0.348 Hom.: 10525

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs701665; hg19: chr6-68894710; COSMIC: COSV69403132;