rs1555091

Variant names:

• chr6-127115500-G-A
• rs1555091
• ENST00000650648.1:n.402-44414C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-127115500-G-A
• chr6-127115500-G-C
• chr6-127115500-G-T

Variant summary

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

The ENST00000650648.1(ENSG00000293110):​n.402-44414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,018 control chromosomes in the GnomAD database, including 7,536 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 0.31 (7536 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 3 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293110	ENST00000650648.1		n.402-44414C>T		intron	N/A
	ENSG00000293110	ENST00000650684.1		n.474-44414C>T		intron	N/A
	ENSG00000293110	ENST00000650727.1		n.441-44414C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46650 AN: 151900 Hom.: 7534 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.307 AC: 46673 AN: 152018 Hom.: 7536 Cov.: 32 AF XY: 0.308 AC XY: 22915 AN XY: 74304

African (AFR) AF: 0.366 AC: 15173 AN: 41466

American (AMR) AF: 0.337 AC: 5152 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2498 AN: 5166

South Asian (SAS) AF: 0.345 AC: 1657 AN: 4808

European-Finnish (FIN) AF: 0.226 AC: 2383 AN: 10552

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17753 AN: 67970

Other (OTH) AF: 0.306 AC: 644 AN: 2108

Alfa AF: 0.255 Hom.: 2698

Bravo AF: 0.322

Asia WGS AF: 0.367 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1555091;

hg19: chr6-127436645;