rs1213366

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-77467153-G-A
• chr6-77467153-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377864	XM_047419658.1	c.-7480G>A		5_prime_UTR_variant	Exon 1 of 6		XP_047275614.1
LOC105377864	XM_047419659.1	c.-7306G>A		5_prime_UTR_variant	Exon 2 of 6		XP_047275615.1
LOC105377864	XM_047419660.1	c.-3742-7373G>A		intron_variant	Intron 5 of 8		XP_047275616.1
LOC105377864	XM_047419661.1	c.-3917+4035G>A		intron_variant	Intron 1 of 5		XP_047275617.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296750	ENST00000741553.1	n.231+337G>A		intron_variant	Intron 1 of 3
ENSG00000296750	ENST00000741554.1	n.124+333G>A		intron_variant	Intron 1 of 3
ENSG00000296734	ENST00000741460.1	n.-206C>T		upstream_gene_variant

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 v4.3

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;