rs6913660

Variant names:

• chr6-27123646-C-A
• rs6913660
• ENST00000607124.2:c.*2820G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-27123646-C-A
• chr6-27123646-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607124.2(H2BC11):​c.*2820G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,804 control chromosomes in the GnomAD database, including 1,575 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 0.14 (1575 hom., cov: 32)
• Consequence: H2BC11 ENST00000607124.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 44 publications found

Genes affected

H2BC11 (HGNC:4761): (H2B clustered histone 11) Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the histone microcluster on chromosome 6p21.33. [provided by RefSeq, Aug 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
H2BC11	ENST00000607124.2	c.*2820G>T		3_prime_UTR_variant	Exon 2 of 2	3		ENSP00000476136.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20940 AN: 151686 Hom.: 1575 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.00887

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.138 AC: 20940 AN: 151804 Hom.: 1575 Cov.: 32 AF XY: 0.132 AC XY: 9764 AN XY: 74180

African (AFR) AF: 0.135 AC: 5597 AN: 41372

American (AMR) AF: 0.105 AC: 1605 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3470

East Asian (EAS) AF: 0.00889 AC: 46 AN: 5174

South Asian (SAS) AF: 0.0924 AC: 445 AN: 4814

European-Finnish (FIN) AF: 0.0908 AC: 953 AN: 10492

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11529 AN: 67912

Other (OTH) AF: 0.123 AC: 259 AN: 2108

Alfa AF: 0.156 Hom.: 3317

Bravo AF: 0.139

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.73
DANN	Benign	0.50
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs6913660; hg19: chr6-27091425;