chr6-38706674-G-A

Variant names:

• chr6-38706674-G-A
• rs1937780
• ENST00000755274.1:n.481-7560G>A

Variant summary

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

The ENST00000755274.1(ENSG00000298390):​n.481-7560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,112 control chromosomes in the GnomAD database, including 7,464 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 (7464 hom., cov: 32)
• Consequence: ENSG00000298390 ENST00000755274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714
• Publications: 12 publications found

Genes affected

ENSG00000298390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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
ENSG00000298390	ENST00000755274.1	n.481-7560G>A		intron_variant	Intron 2 of 2
ENSG00000298390	ENST00000755275.1	n.144+3208G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42364 AN: 151994 Hom.: 7464 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0879

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.279 AC: 42365 AN: 152112 Hom.: 7464 Cov.: 32 AF XY: 0.276 AC XY: 20546 AN XY: 74348

African (AFR) AF: 0.0811 AC: 3367 AN: 41520

American (AMR) AF: 0.271 AC: 4134 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1344 AN: 3466

East Asian (EAS) AF: 0.0882 AC: 458 AN: 5190

South Asian (SAS) AF: 0.246 AC: 1189 AN: 4824

European-Finnish (FIN) AF: 0.363 AC: 3837 AN: 10556

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26871 AN: 67968

Other (OTH) AF: 0.290 AC: 610 AN: 2106

Alfa AF: 0.361 Hom.: 6472

Bravo AF: 0.260

Asia WGS AF: 0.161 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.0
DANN	Benign	0.58
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs1937780; hg19: chr6-38674450;