chr1-170861504-A-G

Position:

• chr1-170861504-A-G

Variant summary

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

The ENST00000669750.1(ENSG00000231424):​n.534-53900T>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 0.48 in 152,018 control chromosomes in the GnomAD database, including 18,102 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 0.48 (18102 hom., cov: 32)
• Consequence: ENST00000669750.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.637 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
	ENST00000669750.1	n.534-53900T>C		intron_variant, non_coding_transcript_variant
	ENST00000664920.1	n.682-53900T>C		intron_variant, non_coding_transcript_variant
	ENST00000670085.1	n.372-53900T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72921 AN: 151902 Hom.: 18080 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.480 AC: 72982 AN: 152018 Hom.: 18102 Cov.: 32 AF XY: 0.488 AC XY: 36251 AN XY: 74296

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.501

Alfa AF: 0.470 Hom.: 2556

Bravo AF: 0.477

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs983215; hg19: chr1-170830645;