6-77474658-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105377864 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377864	XM_047419658.1	c.-3791+7G>T		splice_region_variant, intron_variant	Intron 2 of 5		XP_047275614.1
LOC105377864	XM_047419659.1	c.-3617+7G>T		splice_region_variant, intron_variant	Intron 3 of 5		XP_047275615.1
LOC105377864	XM_047419660.1	c.-3617+7G>T		splice_region_variant, intron_variant	Intron 6 of 8		XP_047275616.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.491

Alfa AF: 0.409 Hom.: 22775

Bravo AF: 0.561

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1936158; hg19: chr6-78184375;