rs1213371

Variant names:

• chr6-77470328-T-C
• rs1213371
• XM_047419658.1:c.-4305T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-77470328-T-C
• chr6-77470328-T-G

Variant summary

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

The XM_047419658.1(LOC105377864):​c.-4305T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.662 in 152,056 control chromosomes in the GnomAD database, including 35,138 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 (35138 hom., cov: 32)
• Consequence: LOC105377864 XM_047419658.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 9 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 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+3512T>C		intron	N/A
	ENSG00000296750	ENST00000741554.1		n.124+3508T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100563 AN: 151938 Hom.: 35095 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.662 AC: 100664 AN: 152056 Hom.: 35138 Cov.: 32 AF XY: 0.660 AC XY: 49072 AN XY: 74308

African (AFR) AF: 0.880 AC: 36522 AN: 41508

American (AMR) AF: 0.632 AC: 9650 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1659 AN: 3466

East Asian (EAS) AF: 0.870 AC: 4495 AN: 5164

South Asian (SAS) AF: 0.569 AC: 2745 AN: 4822

European-Finnish (FIN) AF: 0.547 AC: 5767 AN: 10548

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37891 AN: 67968

Other (OTH) AF: 0.612 AC: 1294 AN: 2114

Alfa AF: 0.581 Hom.: 13646

Bravo AF: 0.677

Asia WGS AF: 0.731 AC: 2541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.99
DANN	Benign	0.42
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1213371; hg19: chr6-78180045;