rs1983722

Variant names:

• chr6-93450974-G-A
• rs1983722
• ENST00000668367.1:n.151+33873G>A

Variant summary

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

The ENST00000668367.1(ENSG00000287683):​n.151+33873G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 151,910 control chromosomes in the GnomAD database, including 683 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 0.085 (683 hom., cov: 31)
• Consequence: ENSG00000287683 ENST00000668367.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179
• Publications: 1 publications found

Genes affected

ENSG00000287683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377899	XR_001744262.2	n.1220+3338G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287683	ENST00000668367.1	n.151+33873G>A		intron_variant	Intron 1 of 4
ENSG00000287683	ENST00000776530.1	n.169+33873G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0854 AC: 12960 AN: 151794 Hom.: 683 Cov.: 31

Gnomad AFR AF: 0.0263

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0717

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

GnomAD4 genome AF: 0.0853 AC: 12957 AN: 151910 Hom.: 683 Cov.: 31 AF XY: 0.0872 AC XY: 6476 AN XY: 74248

African (AFR) AF: 0.0263 AC: 1091 AN: 41484

American (AMR) AF: 0.0971 AC: 1478 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0309 AC: 107 AN: 3462

East Asian (EAS) AF: 0.101 AC: 520 AN: 5136

South Asian (SAS) AF: 0.0910 AC: 439 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10570

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7531 AN: 67906

Other (OTH) AF: 0.0714 AC: 150 AN: 2100

Alfa AF: 0.102 Hom.: 600

Bravo AF: 0.0780

Asia WGS AF: 0.0920 AC: 325 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	0.96
DANN	Benign	0.61
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1983722; hg19: chr6-94160692;