rs4655385

Positions:

• chr1-214950280-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000658732.1(ENSG00000287008):​n.1728+1644A>G 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 0.00904 in 152,278 control chromosomes in the GnomAD database, including 33 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 0.0090 (33 hom., cov: 32)
• Consequence: ENST00000658732.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.695

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00904 (1376/152278) while in subpopulation EAS AF= 0.0458 (237/5178). AF 95% confidence interval is 0.041. There are 33 homozygotes in gnomad4. There are 753 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 33 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904510	XR_007066877.1	n.116+1644A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658732.1	n.1728+1644A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00906 AC: 1378 AN: 152160 Hom.: 33 Cov.: 32

Gnomad AFR AF: 0.00186

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.00705

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00318

Gnomad OTH AF: 0.00574

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

GnomAD4 genome AF: 0.00904 AC: 1376 AN: 152278 Hom.: 33 Cov.: 32 AF XY: 0.0101 AC XY: 753 AN XY: 74462

Gnomad4 AFR AF: 0.00185

Gnomad4 AMR AF: 0.0428

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0458

Gnomad4 SAS AF: 0.00684

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.00318

Gnomad4 OTH AF: 0.00521

Alfa AF: 0.0141 Hom.: 32

Bravo AF: 0.0119

Asia WGS AF: 0.0260 AC: 91 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4655385; hg19: chr1-215123623;