chr6-77464103-G-T

Variant names:

• chr6-77464103-G-T
• rs1228814
• XM_047419658.1:c.-10530G>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.-10530G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,078 control chromosomes in the GnomAD database, including 11,741 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 0.37 (11741 hom., cov: 33)
• Consequence: LOC105377864 XM_047419658.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 14 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=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377864	XM_047419658.1	c.-10530G>T		5_prime_UTR_variant	Exon 1 of 6		XP_047275614.1
LOC105377864	XM_047419659.1	c.-10356G>T		5_prime_UTR_variant	Exon 2 of 6		XP_047275615.1
LOC105377864	XM_047419660.1	c.-3742-10423G>T		intron_variant	Intron 5 of 8		XP_047275616.1
LOC105377864	XM_047419661.1	c.-3917+985G>T		intron_variant	Intron 1 of 5		XP_047275617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296734	ENST00000741460.1	n.48+2797C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56546 AN: 151956 Hom.: 11745 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.372 AC: 56573 AN: 152078 Hom.: 11741 Cov.: 33 AF XY: 0.375 AC XY: 27845 AN XY: 74346

African (AFR) AF: 0.201 AC: 8360 AN: 41526

American (AMR) AF: 0.400 AC: 6122 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1872 AN: 3468

East Asian (EAS) AF: 0.183 AC: 936 AN: 5112

South Asian (SAS) AF: 0.462 AC: 2226 AN: 4816

European-Finnish (FIN) AF: 0.482 AC: 5111 AN: 10610

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30497 AN: 67950

Other (OTH) AF: 0.418 AC: 882 AN: 2110

Alfa AF: 0.272 Hom.: 690

Bravo AF: 0.359

Asia WGS AF: 0.314 AC: 1093 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	13
DANN	Benign	0.92
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1228814; hg19: chr6-78173820;