rs17664743

Variant names:

• chr7-50214301-G-A
• rs17664743
• ENST00000639870.1:n.215-10235C>T

Variant summary

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

The ENST00000639870.1(ENSG00000231681):​n.215-10235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,184 control chromosomes in the GnomAD database, including 5,063 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 0.24 (5063 hom., cov: 33)
• Consequence: ENSG00000231681 ENST00000639870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

Genes affected

ENSG00000231681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 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
ENSG00000231681	ENST00000639870.1	n.215-10235C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36381 AN: 152066 Hom.: 5064 Cov.: 33

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.239 AC: 36406 AN: 152184 Hom.: 5063 Cov.: 33 AF XY: 0.239 AC XY: 17777 AN XY: 74406

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.284

Alfa AF: 0.221 Hom.: 1056

Bravo AF: 0.253

Asia WGS AF: 0.317 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.62
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17664743; hg19: chr7-50253897;