rs7677662

Variant names:

• chr4-144591901-A-G
• rs7677662
• ENST00000649263.1:n.328-175923T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000649263.1(ENSG00000285713):​n.328-175923T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,196 control chromosomes in the GnomAD database, including 2,651 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 0.17 (2651 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 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
ENSG00000285713	ENST00000649263.1	n.328-175923T>C		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.222+163256T>C		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25854 AN: 152078 Hom.: 2650 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.170 AC: 25880 AN: 152196 Hom.: 2651 Cov.: 32 AF XY: 0.170 AC XY: 12653 AN XY: 74418

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.164

Alfa AF: 0.131 Hom.: 2978

Bravo AF: 0.177

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7677662; hg19: chr4-145513053;