chr1-193541697-T-C

Position:

• chr1-193541697-T-C

Variant summary

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

The ENST00000656143.1(ENSG00000227240):​n.153+68321T>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 0.578 in 152,014 control chromosomes in the GnomAD database, including 26,187 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 0.58 (26187 hom., cov: 32)
• Consequence: ENST00000656143.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.877

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5234+68321T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656143.1	n.153+68321T>C		intron_variant, non_coding_transcript_variant
	ENST00000691564.1	n.253-4351T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87798 AN: 151896 Hom.: 26133 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.578 AC: 87913 AN: 152014 Hom.: 26187 Cov.: 32 AF XY: 0.579 AC XY: 43021 AN XY: 74292

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.589

Alfa AF: 0.529 Hom.: 28920

Bravo AF: 0.587

Asia WGS AF: 0.688 AC: 2391 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1007460; hg19: chr1-193510827;