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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668367.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287683	ENST00000668367.1		n.151+33873G>A		intron	N/A
	ENSG00000287683	ENST00000776530.1		n.169+33873G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1983722;

hg19: chr6-94160692;