chr1-5600949-T-A

Position:

• chr1-5600949-T-A

Variant summary

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

The ENST00000637702.1(ENSG00000236948):​n.116-37594A>T 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 0.447 in 151,948 control chromosomes in the GnomAD database, including 16,688 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 0.45 (16688 hom., cov: 33)
• Consequence: ENST00000637702.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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
	ENST00000637702.1	n.116-37594A>T		intron_variant, non_coding_transcript_variant		2
	ENST00000413887.1	n.156-13374A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67915 AN: 151830 Hom.: 16656 Cov.: 33

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.447 AC: 67995 AN: 151948 Hom.: 16688 Cov.: 33 AF XY: 0.440 AC XY: 32663 AN XY: 74248

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.436

Alfa AF: 0.417 Hom.: 1781

Bravo AF: 0.465

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.39
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7528859; hg19: chr1-5661009;