6-77467153-G-A

Variant names:

• chr6-77467153-G-A
• rs1213366
• XM_047419658.1:c.-7480G>A

Variant summary

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

The XM_047419658.1(LOC105377864):​c.-7480G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,060 control chromosomes in the GnomAD database, including 35,308 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 0.66 (35308 hom., cov: 32)
• Consequence: LOC105377864 XM_047419658.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 12 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296750	ENST00000741553.1		n.231+337G>A		intron	N/A
	ENSG00000296750	ENST00000741554.1		n.124+333G>A		intron	N/A
	ENSG00000296734	ENST00000741460.1		n.-206C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100873 AN: 151942 Hom.: 35268 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.664 AC: 100971 AN: 152060 Hom.: 35308 Cov.: 32 AF XY: 0.662 AC XY: 49193 AN XY: 74298

African (AFR) AF: 0.880 AC: 36559 AN: 41534

American (AMR) AF: 0.633 AC: 9665 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1680 AN: 3466

East Asian (EAS) AF: 0.870 AC: 4486 AN: 5154

South Asian (SAS) AF: 0.573 AC: 2756 AN: 4812

European-Finnish (FIN) AF: 0.546 AC: 5766 AN: 10562

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.561 AC: 38119 AN: 67948

Other (OTH) AF: 0.615 AC: 1296 AN: 2106

Alfa AF: 0.624 Hom.: 11362

Bravo AF: 0.679

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.38
DANN	Benign	0.70
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1213366; hg19: chr6-78176870;