rs1321311

Variant names:

• chr6-36655123-C-A
• rs1321311
• ENST00000778909.1:n.192+5558G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-36655123-C-A
• chr6-36655123-C-G
• chr6-36655123-C-T

Variant summary

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

The ENST00000778909.1(ENSG00000301446):​n.192+5558G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,150 control chromosomes in the GnomAD database, including 6,495 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 0.28 (6495 hom., cov: 32)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 102 publications found

Genes affected

ENSG00000301446 (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 (AFR) allele frequency at 95% confidence interval = 0.39 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
ENSG00000301446	ENST00000778909.1	n.192+5558G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42871 AN: 152032 Hom.: 6469 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.282 AC: 42943 AN: 152150 Hom.: 6495 Cov.: 32 AF XY: 0.278 AC XY: 20699 AN XY: 74388

African (AFR) AF: 0.395 AC: 16377 AN: 41486

American (AMR) AF: 0.235 AC: 3597 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1244 AN: 3468

East Asian (EAS) AF: 0.171 AC: 884 AN: 5180

South Asian (SAS) AF: 0.324 AC: 1559 AN: 4816

European-Finnish (FIN) AF: 0.191 AC: 2030 AN: 10604

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16361 AN: 67990

Other (OTH) AF: 0.314 AC: 660 AN: 2102

Alfa AF: 0.255 Hom.: 23936

Bravo AF: 0.285

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.70
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1321311; hg19: chr6-36622900;