rs7221341

Variant names:

• chr17-78335390-T-C
• rs7221341
• ENST00000586321.1:n.61-8575T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-78335390-T-C
• chr17-78335390-T-G

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.61-8575T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,968 control chromosomes in the GnomAD database, including 32,657 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 0.65 (32657 hom., cov: 30)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738
• Publications: 13 publications found

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.74-8575T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.61-8575T>C		intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1	n.39-8575T>C		intron_variant	Intron 1 of 1
ENSG00000267737	ENST00000823931.1	n.72-8575T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98642 AN: 151850 Hom.: 32624 Cov.: 30

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.650 AC: 98726 AN: 151968 Hom.: 32657 Cov.: 30 AF XY: 0.657 AC XY: 48835 AN XY: 74274

African (AFR) AF: 0.605 AC: 25075 AN: 41442

American (AMR) AF: 0.688 AC: 10503 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1824 AN: 3466

East Asian (EAS) AF: 0.987 AC: 5113 AN: 5180

South Asian (SAS) AF: 0.722 AC: 3475 AN: 4812

European-Finnish (FIN) AF: 0.729 AC: 7695 AN: 10550

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43036 AN: 67942

Other (OTH) AF: 0.638 AC: 1347 AN: 2112

Alfa AF: 0.634 Hom.: 59127

Bravo AF: 0.646

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.68
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs7221341; hg19: chr17-76331471;