rs1487441

Variant names:

• chr6-98106018-G-A
• rs1487441
• ENST00000606913.5:n.240+6748G>A

Variant summary

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

The ENST00000606913.5(ENSG00000271860):​n.240+6748G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,738 control chromosomes in the GnomAD database, including 12,728 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 0.39 (12728 hom., cov: 32)
• Consequence: ENSG00000271860 ENST00000606913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 23 publications found

Genes affected

ENSG00000271860 (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 (NFE) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271860	ENST00000606913.5	n.240+6748G>A		intron_variant	Intron 2 of 4	5
ENSG00000271860	ENST00000607032.1	n.410+6748G>A		intron_variant	Intron 4 of 7	3
ENSG00000271860	ENST00000607823.5	n.352+6748G>A		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59663 AN: 151620 Hom.: 12734 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.393 AC: 59649 AN: 151738 Hom.: 12728 Cov.: 32 AF XY: 0.391 AC XY: 28974 AN XY: 74136

African (AFR) AF: 0.232 AC: 9594 AN: 41348

American (AMR) AF: 0.350 AC: 5343 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1865 AN: 3466

East Asian (EAS) AF: 0.407 AC: 2098 AN: 5150

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4814

European-Finnish (FIN) AF: 0.491 AC: 5159 AN: 10502

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32901 AN: 67906

Other (OTH) AF: 0.393 AC: 826 AN: 2102

Alfa AF: 0.459 Hom.: 22387

Bravo AF: 0.379

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1487441; hg19: chr6-98553894;