rs6662385

chr1-72707892-C-T

Variant summary

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

The ENST00000668734.1(ENSG00000225087):n.415+41274G>A 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 0.522 in 151,582 control chromosomes in the GnomAD database, including 25,606 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 0.52 (25606 hom., cov: 32)
• Consequence: ENST00000668734.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378798	XR_947515.3	n.457-6829G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668734.1	n.415+41274G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79190 AN: 151466 Hom.: 25619 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.522 AC: 79172 AN: 151582 Hom.: 25606 Cov.: 32 AF XY: 0.521 AC XY: 38595 AN XY: 74086

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.552

Alfa AF: 0.563 Hom.: 5024

Bravo AF: 0.502

Asia WGS AF: 0.353 AC: 1228 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.5
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6662385; hg19: chr1-73173575;