XM_047419658.1:c.-3791+7G>T

Variant names:

• chr6-77474658-G-T
• rs1936158
• XM_047419658.1:c.-3791+7G>T

Variant summary

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

The XM_047419658.1(LOC105377864):​c.-3791+7G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,986 control chromosomes in the GnomAD database, including 24,661 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 0.53 (24661 hom., cov: 31)
• Consequence: LOC105377864 XM_047419658.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 10 publications found

Genes affected

LOC105377864 (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 (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741553.1. 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
	ENSG00000296750	ENST00000741553.1		n.357+7G>T		splice_region intron	N/A
	ENSG00000296750	ENST00000741554.1		n.217+7G>T		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.533 AC: 81003 AN: 151864 Hom.: 24634 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.534 AC: 81088 AN: 151986 Hom.: 24661 Cov.: 31 AF XY: 0.531 AC XY: 39458 AN XY: 74264

African (AFR) AF: 0.830 AC: 34410 AN: 41474

American (AMR) AF: 0.539 AC: 8233 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.710 AC: 3639 AN: 5126

South Asian (SAS) AF: 0.480 AC: 2312 AN: 4812

European-Finnish (FIN) AF: 0.333 AC: 3520 AN: 10568

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25941 AN: 67940

Other (OTH) AF: 0.491 AC: 1039 AN: 2114

Alfa AF: 0.437 Hom.: 39293

Bravo AF: 0.561

Asia WGS AF: 0.601 AC: 2091 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	2.9
DANN	Benign	0.74
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1936158; hg19: chr6-78184375;