1-56437871-C-A

Position:

• chr1-56437871-C-A

Variant summary

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

The ENST00000641035.1(ENSG00000260971):​n.555+39262G>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 0.347 in 152,060 control chromosomes in the GnomAD database, including 9,260 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 0.35 (9260 hom., cov: 32)
• Consequence: ENST00000641035.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904185	XR_007066106.1	n.5451-25344G>T		intron_variant, non_coding_transcript_variant
LOC124904185	XR_007066104.1	n.7204-9449G>T		intron_variant, non_coding_transcript_variant
LOC124904185	XR_007066105.1	n.3053-9449G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000641035.1	n.555+39262G>T		intron_variant, non_coding_transcript_variant
	ENST00000641346.1	c.*96-37604G>T		intron_variant, NMD_transcript_variant				ENSP00000493280	A2
	ENST00000641415.1	c.*95+45392G>T		intron_variant, NMD_transcript_variant				ENSP00000492943	A2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52690 AN: 151942 Hom.: 9261 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.347 AC: 52715 AN: 152060 Hom.: 9260 Cov.: 32 AF XY: 0.354 AC XY: 26298 AN XY: 74330

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.333

Alfa AF: 0.322 Hom.: 4748

Bravo AF: 0.339

Asia WGS AF: 0.454 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10789021; hg19: chr1-56903543;