rs7221341

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586321.1(ENSG00000267737):​n.61-8575T>C variant causes a intron, non coding transcript 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: ENST00000586321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000586321.1	n.61-8575T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.638

Alfa AF: 0.634 Hom.: 43200

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7221341; hg19: chr17-76331471;